SNP discovery via 454 transcriptome sequencing
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Open Access
- 27 July 2007
- journal article
- research article
- Published by Wiley in The Plant Journal
- Vol. 51 (5) , 910-918
- https://doi.org/10.1111/j.1365-313x.2007.03193.x
Abstract
Summary: A massively parallel pyro‐sequencing technology commercialized by 454 Life Sciences Corporation was used to sequence the transcriptomes of shoot apical meristems isolated from two inbred lines of maize using laser capture microdissection (LCM). A computational pipeline that uses the POLYBAYES polymorphism detection system was adapted for 454 ESTs and used to detect SNPs (single nucleotide polymorphisms) between the two inbred lines. Putative SNPs were computationally identified using 260 000 and 280 000 454 ESTs from the B73 and Mo17 inbred lines, respectively. Over 36 000 putative SNPs were detected within 9980 unique B73 genomic anchor sequences (MAGIs). Stringent post‐processing reduced this number to > 7000 putative SNPs. Over 85% (94/110) of a sample of these putative SNPs were successfully validated by Sanger sequencing. Based on this validation rate, this pilot experiment conservatively identified > 4900 valid SNPs within > 2400 maize genes. These results demonstrate that 454‐based transcriptome sequencing is an excellent method for the high‐throughput acquisition of gene‐associated SNPs.Keywords
This publication has 45 references indexed in Scilit:
- Nearly Identical Paralogs: Implications for Maize (Zea mays L.) Genome EvolutionGenetics, 2007
- Gene discovery and annotation using LCM-454 transcriptome sequencingGenome Research, 2006
- Genetic Dissection of Intermated Recombinant Inbred Lines Using a New Genetic Map of MaizeGenetics, 2006
- Cis-transcriptional Variation in Maize Inbred Lines B73 and Mo17 Leads to Additive Expression Patterns in the F1 HybridGenetics, 2006
- SNPdetector: A Software Tool for Sensitive and Accurate SNP DetectionPLoS Computational Biology, 2005
- Types and Frequencies of Sequencing Errors in Methyl-Filtered and High C0t Maize Genome Survey SequencesPlant Physiology, 2004
- Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.)Molecular Genetics and Genomics, 2003
- Detection of regulatory variation in mouse genesNature Genetics, 2002
- Methods for Genotyping Single Nucleotide PolymorphismsAnnual Review of Genomics and Human Genetics, 2001
- A map of human genome sequence variation containing 1.42 million single nucleotide polymorphismsNature, 2001